enable name-based lookup for EOL offline taxon matcher

jhpoelen commented 4 months ago

related to #11

Currently, EOL ids can be resolved against the EOL taxonomy support.

Desired is to enable name based alignment using the EOL taxonomy support.

e.g.,

echo -e "\tHomo sapiens"\
 | nomer append eol

jhpoelen commented 4 months ago

Just in case, I put a copy of Dynamic Hierarchy at:

Encyclopedia of Life. (2024). Repackaged Encyclopedia of Life (EOL) Dynamic Hierarchy hash://sha256/f91877189f3cd14f4066b16b693a5f93105fd23b881b0825d6781be6ac674b88 hash://md5/18ca6625cf1d24093dc104851ab5722b (2.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12695294

jhpoelen commented 4 months ago

Nomer v0.5.13 now supported name based alignments as well as synonym resolution.

e.g.,

echo -e "\tArius felis"\
 | nomer append --include-header eol\
 | mlr --itsvlite --omd cat

providedExternalId	providedName	relationName	resolvedExternalId	resolvedName	resolvedAuthorship	resolvedRank	resolvedCommonNames	resolvedPath	resolvedPathIds	resolvedPathNames	resolvedPathAuthorships	resolvedExternalUrl
	Arius felis	SAME_AS	EOL:223038	Ariopsis felis	(Linnaeus 1766)	species		Life \| Cellular Organisms \| Eukaryota \| Opisthokonta \| Metazoa \| Bilateria \| Deuterostomia \| Chordata \| Vertebrata \| Gnathostomata \| Osteichthyes \| Actinopterygii \| Neopterygii \| Teleostei \| Otomorpha \| Ostariophysi \| Siluriformes \| Siluroidei \| Ariidae \| Ariopsis \| Ariopsis felis	EOL:2913056 \| EOL:6061725 \| EOL:2908256 \| EOL:2910700 \| EOL:1 \| EOL:3014411 \| EOL:8814528 \| EOL:694 \| EOL:2774383 \| EOL:46557929 \| EOL:2775704 \| EOL:1905 \| EOL:2775792 \| EOL:46582210 \| EOL:40045862 \| EOL:2778397 \| EOL:5083 \| EOL:40051895 \| EOL:5115 \| EOL:47065416 \| EOL:223038	\| \| domain \| \| kingdom \| \| \| phylum \| subphylum \| \| \| class \| subclass \| infraclass \| \| \| order \| suborder \| family \| genus \| species	\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| (Linnaeus 1766)	http://eol.org/pages/223038

fyi @katjaschulz @jhammock

globalbioticinteractions / nomer

enable name-based lookup for EOL offline taxon matcher #184